[pyngl-talk] missing shared library for PyNIO
Kevin Hallock
hallock at ucar.edu
Thu Feb 9 13:07:00 MST 2017
Hi Marcia,
Could you please try running the following command:
conda create -n myenv2 -c conda-forge --file package-list.txt
Hopefully including the conda-forge channel in that command will help find the missing packages.
Kevin
> On Feb 9, 2017, at 12:41 PM, Marcia Branstetter <branstetterm at ornl.gov> wrote:
>
> Hi Kevin,
>
> I tried this, but got an error message when I tried to create the new myenv2:
>
> [mbranst at or-condo-login02 ~]$ conda create -n myenv2 --file package-list.txt
> Fetching package metadata .........
>
>
> PackageNotFoundError: Package not found: '' Package missing in current linux-64 channels:
> - ca-certificates 2016.9.26 0
>
> You can search for packages on anaconda.org with
>
> anaconda search -t conda ca-certificates
>
> You may need to install the anaconda-client command line client with
>
> conda install anaconda-client
> -------------------------------------------------
> I tried those suggestions, but still kept getting the same error.
>
> Thanks,
> Marcia
>
> On Wed, 8 Feb 2017, Kevin Hallock wrote:
>
>> Hi Marcia,
>> The conda-forge automated build system is currently having issues building a
>> new version of PyNGL, although PyNIO was successfully rebuilt yesterday. The
>> problem now is that certain packages that both PyNIO and PyNGL depend on
>> have been updated.
>> I have tried to create an environment containing both PyNIO and PyNGL using
>> older dependencies, but I have not been able to find a working combination
>> of dependencies (although I am certain one exists).
>> PyNIO is currently working if you do not also install PyNGL, and I have been
>> working with conda-forge to get the new version of PyNGL released as soon as
>> possible.
>> If you still have access to the conda environment that worked for you
>> several weeks ago, you could try the following (an example from “conda list
>> --help”):
>> Save packages for future use:
>> conda list --export > package-list.txt
>> Reinstall packages from an export file:
>> conda create -n myenv --file package-list.txt
>> I have no experience using “conda list” and “conda create” like this, but it
>> might allow you to duplicate the environment you had before.
>> I’m sorry for the inconvenience, hopefully we’ll have PyNGL working again
>> shortly.
>> Kevin
>>
>> On Feb 8, 2017, at 1:31 PM, Marcia Branstetter
>> <branstetterm at ornl.gov> wrote:
>> Hi Kevin,
>> Here is the output:
>> [mbranst at or-condo-login02 ~]$ conda list -n pyn_test
>> # packages in environment at /home/mbranst/miniconda2/envs/pyn_test:
>> #
>> bzip2 1.0.6 3
>> ca-certificates 2016.9.26 0
>> conda-forge
>> cairo 1.14.6 0
>> conda-forge
>> certifi 2016.2.28 py27_0
>> curl 7.52.1 0
>> expat 2.1.0 0
>> fontconfig 2.11.1 6
>> conda-forge
>> freetype 2.6.3 1
>> conda-forge
>> freexl 1.0.2 1
>> conda-forge
>> g2clib 1.6.0 2
>> conda-forge
>> gdal 2.1.3 np111py27_1
>> conda-forge
>> geos 3.5.0 0
>> giflib 5.1.4 0
>> conda-forge
>> gsl 2.2.1 0
>> hdf4 4.2.11 0
>> hdf5 1.8.17 1
>> hdfeos2 2.19.1 7
>> conda-forge
>> hdfeos5 5.1.15 6
>> conda-forge
>> icu 56.1 4
>> conda-forge
>> jasper 1.900.1 4
>> conda-forge
>> jbig 2.1 0
>> jpeg 9b 0
>> json-c 0.12 0
>> conda-forge
>> kealib 1.4.6 0
>> libdap4 3.18.3 2
>> conda-forge
>> libgcc 5.2.0 0
>> libgfortran 3.0.0 1
>> libiconv 1.14 0
>> libnetcdf 4.4.1.1 2
>> conda-forge
>> libpng 1.6.28 0
>> conda-forge
>> libpq 9.5.4 0
>> libspatialite 4.3.0a 14
>> conda-forge
>> libtiff 4.0.6 3
>> libxml2 2.9.4 0
>> mkl 2017.0.1 0
>> ncl 6.3.0 2
>> conda-forge
>> ncurses 5.9 10
>> numpy 1.11.3 py27_0
>> openjpeg 2.1.2 2
>> conda-forge
>> openssl 1.0.2k 0
>> pcre 8.39 1
>> pip 9.0.1 py27_1
>> pixman 0.34.0 0
>> pkg-config 0.28 1
>> proj4 4.9.3 2
>> conda-forge
>> pyngl 1.5.0_beta20161122 np111py27_1
>> conda-forge
>> pynio 1.5.0_beta20160623 np111py27_14
>> conda-forge
>> python 2.7.13 0
>> readline 6.2 2
>> setuptools 27.2.0 py27_0
>> sqlite 3.13.0 0
>> tk 8.5.18 0
>> udunits2 2.2.23 0
>> conda-forge
>> util-linux 2.21 0
>> wheel 0.29.0 py27_0
>> xerces-c 3.1.4 0
>> xz 5.2.2 1
>> zlib 1.2.8 3
>> Thanks,
>> Marcia
>> On Tue, 7 Feb 2017, Kevin Hallock wrote:
>>
>> Hi Marcia,
>>
>> Could you please run “conda list -n pyn_test” and reply
>> with the output?
>>
>> The conda-forge project has been rebuilding packages the
>> past few days to address issues with libicu like what
>> you’ve experienced.
>>
>> Thanks,
>> Kevin
>>
>> On Feb 7, 2017, at 1:23 PM, Marcia Branstetter
>> <branstetterm at ornl.gov> wrote:
>>
>> Hi,
>>
>> I installed PyNIO and PyNGL on a computer:
>> Linux 3.10.0-327.4.4.el7.x86_64 #1 SMP Tue Jan
>> 5 16:07:00 UTC 2016 x86_64
>> x86_64 x86_64 GNU/Linux
>> today, using
>> conda create --name pyn_test --channel
>> conda-forge pynio
>> pyngl
>>
>> but after I activate pyn_test, go into python
>> and then try to import Nio,
>> I get an error message:
>> import Nio
>>
>> Traceback (most recent call last):
>> File "<stdin>", line 1, in <module>
>> File
>> "/home/mbranst/miniconda2/envs/pyn_test/lib/python2.7/site-packages/PyNIO/N
>> io.py",
>> line 83, in <module>
>> from nio import *
>> ImportError: libicui18n.so.58: cannot open
>> shared object file: No such
>> file or directory
>> import Ngl
>>
>> Segmentation fault (core dumped)
>>
>> If I import Ngl first, and print the version,
>> I get
>> import Ngl
>> print
>> Ngl.__version__
>>
>> 1.5.0_beta20161122
>>
>> A few weeks ago, I installed PyNIO and PyNGL
>> in the same way on another
>> linux machine, and it's been working fine.
>>
>> I tried installing on a linux virtual machine
>> today and got the same
>> errors.
>>
>> Thanks,
>> Marcia Branstetter
>>
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